Multiple long-term, experimentally-evolved populations of Escherichia coliacquire dependence upon citrate as an iron chelator for optimal growth on glucose

Abstract

BackgroundSpecialization for ecological niches is a balance of evolutionary adaptation and its accompanying tradeoffs. Here we focus on the Lenski Long-Term Evolution Experiment, which has maintained cultures of Escherichia coli in the same defined seasonal environment for 50,000 generations. Over this time, much adaptation and specialization to the environment has occurred. The presence of citrate in the growth media selected one lineage to gain the novel ability to utilize citrate as a carbon source after 31,000 generations. Here we test whether other strains have specialized to rely on citrate after 50,000 generations.ResultsWe show that in addition to the citrate-catabolizing strain, three other lineages evolving in parallel have acquired a dependence on citrate for optimal growth on glucose. None of these strains were stimulated indirectly by the sodium present in disodium citrate, nor exhibited even partial utilization of citrate as a carbon source. Instead, all three of these citrate-stimulated populations appear to rely on it as a chelator of iron.ConclusionsThe strains we examine here have evolved specialization to their environment through apparent loss of function. Our results are most consistent with the accumulation of mutations in iron transport genes that were obviated by abundant citrate. The results present another example where a subtle decision in the design of an evolution experiment led to unexpected evolutionary outcomes.

The Ability of Flux Balance Analysis to Predict Evolution of Central Metabolism Scales with the Initial Distance to the Optimum

“…The isolates analyzed in the current experiment consisted of the ancestral line, REL606 [29], as well as the ‘A’ clone from 10 of the 12 lines frozen at 50,000 generations that were used in an earlier paper (A−1 = REL11330; A−2 = REL11333; A−4 = REL11336; A−5 = REL11339; A−6 = REL11389; A+1 = 11392; A+2 = REL11342; A+3 = REL11345; A+4 = REL11348, A+5 = REL11367) [30]. The A−2 clone used is from the ‘large’ lineage that has coexisted with a cross-feeding ‘small’ lineage for tens of thousands of generations [37].…”

“…In terms of using experimental evolution to test optimality, the cultures that have had the greatest time to adapt are those from the E. coli long-term experimental evolution (LTEE) populations that have been evolving in the Lenski laboratory for over 50,000 generations [29], [30]. These twelve replicate populations have evolved in minimal medium with glucose since 1988, experiencing 100-fold daily dilutions that result in a short lag phase, nearly seven consecutive generations in exponential phase, and then stationary phase.…”

Specificity of genome evolution in experimental populations of Escherichia coli evolved at different temperatures

“…Our genetic results and fitness measurements do not rule out that some of the mutations in the clones evolved in one temperature regime reduced fitness in the other temperature regimes; instead, they imply that many of the most common mutations did not impose these tradeoffs. The loss of performance in alternative environments, where selection has not acted to maintain performance, is especially important in populations that evolve hypermutability because many mutations can accumulate that are neutral or nearly so in the current environment but where each has some chance of reducing fitness in other environments (44,45). It is also possible that, had the TEE continued for as long as the LTEE, beneficial mutations in the other treatments would generate highly temperature-specific adaptations that preclude genetic convergence with the 37°C lines.…”

Phenotypic characteristics contributing to the enhanced growth ofEscherichia colibloom strains

“…). The results of these experiments show that the subtraction of iron using dipyridyl reduces the growth rate across genotypes except for cap+fec–, proving that iron enhances bacterial growth, as reported previously (Leiby et al ., ; Braun and Hantke, ; Westrich et al ., ); however, the results do not suggest that the presence of the fec operon plays a key role in determining the growth rate. Rather, the dominant growth response appears to have been caused by the capsule.…”

“…Iron is a limited nutrient and is fundamentally important for bacterial growth (Neilands, ; Braun, ; Leiby et al ., ; Braun and Hantke, ; Westrich et al ., ). Iron received via Saharan dust has been implicated in causing up to a 30‐fold increase in culturable Vibrio in the Caribbean and sub‐tropical Atlantic waters (Westrich et al ., ).…”